Changes to Earth Package
------------------------

4.6.0 Dec 14, 2017

  Added the Auto.linpreds argument. See the earth help page for details.
  Thanks to Ceyda Yazici for help on this.

  Further extensions to argument handling with pmethod="cv"
  (necessary when formula is a local variable in function calling earth.formula).

4.5.1  Jul 26, 2017

  With pmethod="cv", you can now use arguments like "thresh" when earth
  is called in a function for which "thresh" is a local variable.
  Thanks to Matthew Watkins for help on this.

4.5.0  Apr 20, 2017

  Removed trailing NULL entries in R_CMethodDef and R_FortranMethodDef to
  match changes to Rdynload.c in R core source code above version 3.3.3.

4.4.9  Feb 19, 2017

  Fixed missing terminal entry in rentries.c:fortranEntries.
  Minor tweaks to C and Fortran files for clang and vcc warnings.

4.4.8  Feb 18, 2017

  Minor updates to model.matrix.earth:
    Fixed a problem which can occur when the new x is a vector.
    We return NA if variables are missing in newdata.
    Extended the tests for model.matrix.earth in the slowtests directory.

  We now call R_init_earth (to quieten CRAN check complaints).
  To do that, added the file rentries.c and made changes to ForwardPassR.

  Minor documentation updates.  Added DOI references to Friedman's papers
  in the help pages as requested by Uwe Ligges.

4.4.7  Oct 18, 2016

  Updates to the documentation and to the libraries
  shared with plotmo and rpart.plot.

4.4.6  Sep 5, 2016

  Added ... to argument list for all plotmo.* functions
  for compatibility with plotmo version 3.2.0 and higher.

  Tweaked leaps.f to eliminate gfortran warnings about the
  deprecated way that DO loops were terminated.

4.4.5  Aug 19, 2016

  Fixed issue in earth.c with the latest gcc which calculates a
  negative almost-zero GRSq (something like -1e-17).
  This messed up the test scripts because it printed as -0.0000.

  Merged the library source file lib.R with the plotmo and
  rpart.plot packages's lib.R.

  Updated cross-validation section in vignette.

4.4.4  Jan 08, 2016

   Fixed error message when predicting with a weighted model with a factor variable.
   Thanks to Damien Georges.

   Added a few type casts needed for clang and for matrices bigger than 2GB.
   Thanks to Todd Rudick.

   Removed a leftover debug call to cat("gc\n").
   Thanks to Dirk Eddelbuettel.

   Updated some stale web links in the documentation.

4.4.3  Sep 26, 2015

   Minor changes to satisfy CRAN checks.

   The print_summary function now has special handling for lists.

   The stopifnot.identifier function now allows ":" in identifier names.

4.4.2  Jun 24, 2015

   In model.matrix.earth we no longer unnecessarily issue the message:
      variable 'foo' was fitted with type "nmatrix.1"
      but type "numeric" was supplied

4.4.1  Jun 17, 2015

    Fixed an issue with earth's interaction with caret in certain
    situations. Thanks to Alexios Ghalanos for help on this.

    Documentation updates.

4.4.0  May 29, 2015

    Changes to earth.c. The following changes mean that earth will
    produce slightly different models from previous releases:

        o For minspan counting in interaction terms, we now only count cases
          that are supported by the parent term (i.e., cases that are in the zero
          part of the parent hinge are not counted).  This makes earth more
          robust against overfitting on the edges of the training predictor space.
          In previous versions, earth could create a hinge at the edge of the
          predictor space, then crank up the hinge coefficient to a huge
          value because of one or two outlying cases. This is now less likely.
          Thanks to Louise Corron at Universite Aix-Marseille for help
          characterizing this.

        o Modified the code for weighted models, mostly for consistency with
          non-weighted models.

        o Changed a numerical tolerance in FindKnot for better support of
          "sawtooth" responses (responses which sharply zigzag up and down as
          the predictor increases).  The numerical tolerance was changed because
          we were seeing a breakdown caused by the the strategy of "start at one
          end of the predictor range and search downwards for knots".  The
          asymmetrical nature of this search tends to honor potential knots at
          the high end of the predictor range at the expense of knots at the
          low end before numerical tolerances kick in.  Thanks to Greg Jensen
          at Columbia for help on this.

        o Other minor updates, particularly to trace prints. Values that
          are almost zero are now printed as zero, for more consistency
          in trace prints across different architectures.

    The weights argument has now been comprehensively tested and the
    warning "support of weights is provisional" is no longer issued.

    Earth now supports pmethod = "cv", which uses cross-validation to
    select the optimum number of model terms.
    Thanks to the sabermetrician Jonathan Judge for help on this.

    Earth now supports bigger models with less memory thrashing.  It calls
    gc() internally where necessary.  Leverages are calculated only for
    non-big models (since memory use peaks when calculating leverages).

    The model selection plot has had various enhancements.

    Various other minor code and documentation updates.

4.3.0  Apr 30, 2015

    We now support data matrices bigger than 2GB.

    The plot.earth function now invokes plotres in the plotmo package.
    Reparameterized the argument list of plot.earth, but maintained
    back-compatibility by using the "dots" routines.

    Numerous minor code clean-ups.

4.2.0  Jan 12, 2015

  plot.earth:
    o Changed the default color scheme to black and red (was black and lightblue)
      for consistency with plot.lm and similar functions, and for readability.
      A result of this change is that col.line is now once again called col.rsq.
    o The type="pearson" arg is now type="student", since the stddev
      estimated by the varmod now includes a leverage correction.
    o The versus arg now takes numeric values, and can be used to plot
      the residuals versus the response or the leverages.
    o Added "abs" to displayed spearman correlation text to minimize confusion.
    o The error handling for the versus argument is improved.

  minspan and endspan:
    o The positioning of knots is now more symmetrical (in that we now have
      an equal number of skipped cases at each end of the predictor range).
    o We always allow a knot, even if endspan and minspan are such that
      no knots would normally be allowed.
    o Added the Adjust.endspan argument to reduce the possibility of an
      overfitted interaction term supported by just a few cases on the
      boundary of the predictor space.

  variance models:
    o Variance model residuals now use the predicted value instead of the
      mean out-of-fold values.  This is simpler, and gives better results
      in simulation.  A consequence is that the legal values for
      predict.varmod's type argument have changed.
    o The convergence criteria for residual model IRLS was modified and
      non-convergence is better reported.

  The intercept-only RSS with weights is now calculated correctly in earth.c.
  Weights are now better tested.

  The Get.crit argument was removed from earth.fit.  No longer needed.

  RSq's and GRSq's that are within 1e-5 of zero are now set to zero to facilitate
  testing across machines in the presence of numerical error,  especially
  when case weights are used.

  Increased MaxAllowedRssDelta in earth.c because it was a bit too conservative.

  Updated the vignettes and help pages, and some error messages.

4.1.0  Dec 17, 2014

  Added clang to the slowtests suite, and cleaned up minor warnings issued by clang.

  Forward pass termination messages are now similar in R and C code.

  The internal variable "reason" is now named "termcond".

  Documentation improvements.

4.0.0  Dec 12, 2014

  Earth now supports prediction intervals.  See earth's new var.method
  argument, and the new vignette.  The predict.earth function now has
  "interval" and "level" arguments.  The residual plot of plot.earth now
  shows prediction intervals if available.  The new version of plotmo
  will also show earth prediction intervals.

  Case weights are now supported but are not yet comprehensively tested.
  The current implementation of case weights is slow.

  The print.earth and print.summary.earth function now print the reason
  the forward pass terminated.

  The ordering of terms in summary.earth was changed slightly: within
  term pairs, the term for "predictor less than hinge" is now placed
  before the term for "predictor greater than hinge" (so for example,
  h(16-Girth) is before h(Girth-16)}.  This was done to make model
  interpretation slightly easier.

  Predictors that are discovered to best enter linearly (no knot) are
  now printed without a knot by summary.earth, to make model
  interpretation a little easier.  Also, their entry in the dirs matrix
  is now 2, the same as predictors that are forced to enter linearly
  by earth's linpred arg.

  The minspan argument can now take negative values, to specify the
  max number of knots per predictor (as opposed to the spacing between
  the knots).

  Earth now has an endspan argument.  The default endspan=0 gives
  the previous behaviour.

  The linpreds argument now accepts variables specified by name.

  Earth now accepts nk=1 to force an intercept-only model (in previous
  versions, nk had to be at least 3).

  DUP is now always TRUE in internal calls to C function, to satisfy
  CRAN checks.  Sadly, this means that the earth forward pass uses
  more memory (because all the argument data is duplicated when
  handing over to C).

  The comprehensive (but slow) earth tests are now in inst/slowtests.
  As always, the tests in earth/tests just do a basic test of
  portability problems.

  "cv.rsq" is now consistently "CVRSq".

  In the earth C code, QR_TOL is now 1e-7 (was .01) to match
  lm's use of tol=1e-7 for dqrdc2.

  The GLM types for residuals.earth are now prefixed by "glm.",
  and type="pearson" now returns the pearsonized residuals.

  Various other minor tweaks, improvements to error messages, etc.

  Changes to plot.earth:

      plot.earth has some new arguments, including info,
      delever, pearson, level, and versus.

      The which argument now has extra values 5:8, to plot
      residuals vs log fitted values etc.

      The residuals plot now has a symmetrical y axis to make asymmetry
      in the point cloud more obvious (see the center argument).

      Graphics arguments to plot.earth are moved down so the more
      important arguments are earlier.

      plot.earth now has an xlim argument, and the ylim argument can
      now be used on any plot (not just the Model Selection plot),
      providing it is the only plot (length(which == 1).

      Some args are deprecated or changed (you will get an
      informative message if you use them).  The changes were
      made for consistency with similar arguments elsewhere.
          --Old--        --New--
          col.rsq        col.line
          col.residuals  col.points
          nresiduals     npoints
          col.legend     use legend.pos=NA for no legend

      If 1 is in the "which" arg to plot.earth, then ylim is used
      for the Model Selection plot, else it is used for the
      Residuals vs Fitted plot.

3.2-7  Jan 28, 2014
  Tweaks to standalone version of earth for clean compiles with certain 64 GCC builds.
  plot.evimp now works with intercept-only models.
  Other minor tweaks to plot.evimp.
  Clerical changes to satisfy recent CRAN checks.

3.2-6  Apr 15, 2013
  Added format.earth style="C".
  Included the leaps package files into the earth package, to prevent
      warnings from CRAN check about earth's use of internal leaps code.
      Removed "Depends: leaps" from earth's DESCRIPTION file.
  Lin deps discovered by leaps are now slightly better handled.
  Small changes to earth.c and earth.h for stand-alone builds.
  Added sections to the FAQ on using earth for
      binary and categorical responses.
  Added a section to the vignette on building a model
      based on cross validation results.
  Removed trace=4 from test.earth.R so a non-problem is no longer
      reported due to minor numerical differences across architectures.
  Reduced the number of digits printed in some of earth's trace messages.
      This makes trace results more consistent across different architectures
      (the ls digits are often in the numerical noise floor).
  We now print a max of 20 columns of a matrix when tracing.
  The legend.text arg of plot.earth.models now works correctly.

3.2-3  Apr 27, 2012
  Incorporated Glen Luckjiff's patch to fix predict.earth(type="terms")
      failure when bx had just two columns.
  We no longer call fflush when in an R environment.
  The tests/test.earth.R code now uses the tree rather than the ozone1 data,
      in an effort to get test consistency across different architectures.
  Added .Rinstignore to drop inst/docs/figs files (prevents note in CRAN build).

3.2-2  Mar 14, 2012
  We no longer pass R_NilValue from the R code to the C code.
  Incorporated Olaf Mersmann's patch for POS_INF with the INTEL_COMPILER.
  Code touchups for Microsoft Visual Studio 2010.

3.2-1  Jul 19, 2011
  Documentation touchups.

3.2-0  Jun 19, 2011
   The PDF file is now a standard vignette (but with no executable code).
   The "Importances" printed by print.earth are now a maximum of option("width") wide.
   We no longer warn "effective number of GCV parameters >= number of cases"
       but instead set such GCVs to Inf, so GCVs are now always
       non-decreasing with the number of terms.  Documented as FAQ 12.11.
   The earth C routines now print memory allocations if trace=1.5.
   The pnTrace arg to ForwardPassR is now a double and called pTrace (allowing trace=1.5).
   The default nk is now clipped at 200.  This limits the amount of memory
       needed in the forward pass for large x matrices.  Numerical limits
       will probably kick in before 200 are reached anyway.
   We now force Use.beta.cache=FALSE with a message if the beta cache would
       be more than 3 GB.
   summary.earth now warns if illegal arguments are passed.
   Documentation touched up.

3.1-1  Jun 15, 2011
   Documentation emendations.
   We now issue a warning if user uses a CV arg to plot.earth but no CV data to plot.
   The CV summary print no longer prints the response name for single response models.

3.1-0  Jun 14, 2011
   print.evimp now formats the results a little differently (more clearly).
   "Reached min GRSq" and similar trace messages now also print the number of terms.
   The min auto-calculated ylim in model selection plots is now clamped at -1.
   Added the col.residuals, col.pch.max.oof.rsq, and col.pch.cv.rsq args to plot.earth.
   Cross validation with wp no longer gives an error message.
   Revised the documentation.

3.0-0  Jun 10, 2011
   Created the vignette earth-notes.pdf which collects and extends
     documentation that was previously in the help files.
   Revamped cross validation.  New argument "ncross" to earth.
   Extended plot.earth, mostly for cross validation.
   The default for evimp's "sqrt." argument is now TRUE.
   plot.earth now uses lowess rather than loess (loess tends to issue ugly warnings).
   Removed earth's Print.pruning.pass argument.
   Earth now uses less memory if passed an x matrix of doubles.  Earth's memory report
     (with trace>=4) was not accurate in all cases and has been removed.
   Tweaked the Author: entry in DESCRIPTION for better results from citation().
   Other minor touchups.

2.6-2  Apr 25, 2011
   Moved plotmo.methods.earth.R to here so the plotmo package is independent of earth.
   Modified test scripts to conform to R 2.13.0's way of printing numbers.

2.6-1  Apr 13, 2011
   Fixed an issue of dependency on the plotmo package.

2.6-0  Apr 12, 2011
   Moved plotmo to the plotmo package, and added "depends plotmo" to earth's DESCRIPTION
   Added the Exhaustive.tol arg as a work-around for leaps.exhaustive error code -999
      (Thanks to David Marra for help tracking this down.)
   The "Exhaustive pruning" pacifier is now printed based on the number of subsets
   Warnings from leaps routines are now treated as errors (because ret val is bad with warning)
   Replaced n=2 and similar in calls to eval with an explicit environment
   The decision to use eval.subsets.xtx is now more automatic and less obtrusive
   The response y is now named in certain situations where it used to be unnamed
   Removed annoying warning "specified nprune 20 is greater than the number of model terms"
   Some code tidying

2.5-1  Mar 25 2011
   Modified handling of illegal arguments

2.5-0  Mar 24 2011
   Changes to plotmo:
     The arguments were reordered (moved the most important arguments first).
     The ycolumn arg is now called nresponse and handled more consistently.
     The degree2="all" setting is now replaced by all2=TRUE, likewise for degree1.
     The default for the type argument is now object dependent.
     The cex parameter is now supported, and text is a little larger for most plots.
     The degree2 graph titles now have a space for readability.
     There is some minor backwards incompatibility in the minor arguments.
     The plotmo graphs are now ordered on the variable order, for all model classes.
     Plotmo now handles a wider range of object classes.
     Factor predictors are now plotted in degree2 plots.
   Miscellaneous other touchups.

2.4-8  Mar 05 2011
   plotmo now handles vector colors better
   plotmo is now better at plotting lda and qda models
   Added the jitter.response argument to plotmo
   Moved plotmo method functions into a new file, plotmo.methods.R.

2.4-7  Feb 02 2011
   Intercept-only models are now better supported, esp. for earth-glm  models.
   Martin Renner and Keith Woolner provided the impetus for this change.

   Legend arguments are now handled better in plot.earth.models.
   A vector legend.text is now handled correctly and you can use
   values like "topleft" in legend.pos (thanks to Gavin Simpson at ECRC).

   The elements of cv.list in earth's returned value are now named,
   and plot.earth.models(model$cv.list) thus has better legends.

   Cumulative distrib plots in plot.earth.models now use the jitter arg, and
   plot.earth's (pointless) jitter argument has been removed.

   A few code and doc touchups were also made.

2.4-6 Jan 26 2011
    Made the following changes to plotmo:
      We now print the fixed grid values unless trace < 0.
      The degree1 and degree2 arguments now have an "all" option.
      We now have better support for rpart objects
      The cex arg is now also used for response values (with cex.response!=0).
      Added cex.lab argument.
      For factor predictors we now print the factor levels vertically along the x axis.
    Fixed crossed type.gcv and type.rss args in plot.evimp.
    Fixed residuals.earth to handle vector responses correctly.
    (Thanks to Gavin Simpson at UCL for providing fixes for the above bugs.)
    plot.evimp now doesn't use on.exit(par(no.readonly=TRUE)), so we
      now allow subsequent plots on the same page with mfrow != c(1,1).
    Did the usual document touchups.
    Minor cleanups for R check (partial arg matches).

2.4-5 Oct 30 2010
    Plotmo now better handles the "data" argument for earth.formula models.
    (Thanks to Keith Woolner for spotting that this was previously incorrect.)

2.4-4 Oct 6 2010
    NAs are now allowed in the data passed to predict.earth.  The predicted value
    will be NA unless the NAs are in variables that are unused in the earth model.

2.4-3 Sep 29 2010
    For certain data we were seeing duplicated term names for cuts that
    are very close to each other.  To avoid this you can now use
    options(digits) to increase the number of significant digits used
    when forming term names.  (Thanks to Keith Woolner for spotting this.)

2.4-2 Aug 28 2010
    We now give the correct error message for attempted cross validation of
        paired binomial responses (which is not yet supported).
    Labels on the largest residuals in plot.earth graphs are now slightly
        better positioned (using plotrix::thigmophobe.labels).
    plotd now handles qda objects in the same manner as lda objects
    Other doc touchups.

2.4-0 Nov 8 2009
    This version of earth will build models SLIGHTLY DIFFERENT FROM PRIOR VERSIONS,
    because I fixed a bug in the calculation of minspan and endspan.
    Use minspan=-1 for backwards compatibility.
    (Thanks to Gints Jekabsons for spotting this.)

2.3-5 Oct 7 2009
    Fixed bug where glm.control args were ignored under certain circumstances
    (Thanks to Jérôme Guélat for letting me know about this.)

2.3-4 Sep 21 2009
    . Fixed bug where predict.earth of a earth-glm model under R 2.9.0 and higher
      incorrectly gave the message: Object of type 'closure' is not subsettable
      (Thanks to Thomas Brockmeier for help tracking this down.)
    . plotd now correctly ignores the vline if vline.col=0
    . Doc touchups

2.3-2 Mar 23 2009
    Extended plotd
    Doc touchups

2.3-1 Feb 26 2009
    Doc touchups
    Added leaps::: prefix needed for new version of the leaps package
    Added style="max" to summary.earth
    Added labels param to plotd
    Reordered some of earth's arguments

2.3-0 Feb 18 2009
    Added the plotd function
    Removed some restrictions on type="class" in predict.earth
    Added sqrt. argument to evimp
    Added more grid lines to cumul density plot in plot.earth
    Added a help page section on interpreting the graphs in plot.earth
    Miscellaneous other touchups to code and docs

2.2-3 Feb 2 2009
    Added levels to the return value
    Added type=class and thresh arguments to predict.earth
    Thanks to Max Kuhn for suggesting these improvements

2.2-2 Jan 30 2009
    Doc touchups
    Cross validation MaxErr is now signed

2.2-1 Jan 22 2009
    Added cross validation i.e. the nfold and stratify parameters.

    We now scale y before the forward pass, for better numeric stability in
    the forward pass with very big or very small y's.
    For the old behaviour, set earth's new argument scale.y=FALSE.

    Added get.pairs.bagEarth so plotmo prints degree2 plots for caret:bagEarth models.

    Changes internal to earth.c:
        High values of trace argument are treated differently
        ServiceR (to allow interrupts) is called more consistently for large datasets
        Delta RSS handling is simplified
        Changed some var names for consistency
     The last two were a byproduct of experimental changes to earth that
     were not included in this release.

     Changed documentation to American English.

2.1-2 Nov 18 2008
    Touched up evimp help page.

2.1-0 Nov 15 2008
    plotmo now has better support for factors and for glm models
    na.action (always na.fail) is now handled as documented in earth.formula
    Added style="bf" to format.earth and summary.earth
    Fixed a few minor bugs and touched up documentation for evimp

2.0-6 Oct 30 2008
    You can now pass only the needed subset of columns to predict.earth
    Added plot.evimp
    Removed spurious warning "Need as many rows as columns"

2.0-5 Jul 14 2008
    Touched up documentation for format.lm.

2.0-4 June 22 2008
    Touched up code and documentation for a zero thresh value.

2.0-3 June 22 2008

Zero values are now allowed for earth's "thresh" parameter (previously if
    you used thresh=0, thresh was clamped internally to 1e-10).
    Also, if thresh=0, the MAX_GRSQ forward pass condition is ignored.
    The idea is to get as close to a big nk as possible
Changed "valid.names" argument of format.earth and format.lm to "colon.char"
    which achieves the same end more simply.

2.0-2 June 15 2008

Added column names to results of mars.to.earth, allows use of evimp.
Added valid.names argument to format.earth and format.lm.

2.0-1 June 10 2008

Added "namesx" and "first" arguments to the "allowed" function.
evimp() for a scalar x now returns a matrix (I added a missing drop=FALSE).

2.0-0 June 07 2008

Added support for glms and factors (but plotmo does not yet support factors).
Added variable importance function "evimp".
Added response weights argument "wp" to earth.
Output of summary.earth has changed to better deal
   with multiple response models, see the "style" argument.
Added namesx and namesx.org to earth's return value.

1.3-2 Mar 29 2008

Fixed two bad multiple response bugs:
a) for multiple reponse models, earth calculated the wrong null RSS and
   therefore the wrong RSq and GRSq for the sub-models.  (The total
   RSq and GRSq were correct.)
b) the wrong betas were used when pruning multiple response models.

Also fixed a bug where summary.earth printed the wrong number
of cases for multiple response models.

1.3-1 Mar 22 2008

"update.earth" now has a "ponly" argument, to force pruning only.
Because of this change, the "ppenalty" argument to earth is no longer
needed and has been removed.

Revisited text of warnings after I was bamboozled by one of
my own warnings.

Tweaked legend positioning in plot.earth.models.

1.3-0 Mar 18 2008

Default minspan is now 0 (was 1) for compatibility with mda:mars and
Friedman's MARS paper (I've flip flopped on this one).  This means
that models built with the default args will be little different to
before.

Earth's peak memory is now about 40% less.

Big models are now more responsive to ^C.

For multiple response models, we now print response names in most
places instead of just "Response N".

Removed get.nterms.per.degree and get.nused.preds.per.subset from
NAMESPACE and from help pages, to simplify user interface.

Fixed some niggling document issues and extended the FAQ.

1.2-2 Jan 2008

print.summary.earth now prints the call even for x,y interface to earth
plotmo now accepts x matrices without column names
Tweaked FindKnot and OrthogResiduals for speed
Removed a few shadowed variables in earth.c after running gcc -Wshadow
Clarified some paras in earth.Rd, reduced page width for better html display

1.2-1

Fixed a newvar.penalty bug introduced in previous release.
Added src/tests/test.earthmain.gcc.bat
More man page tweaks

1.2-0

Added linpreds, allowed, and Use.beta.cache arguments
Anova decomp is now more consistent
Added a few GPL headers
Reinstated the beta cache
More man page tweaks

1.1-5

Fixed bug reported by Joe Ritzer: long predictor names got munged in plotmo
Changed "class" to "response" throughout when used for the
predicted responses in the input y.
Man page tweaks based on user feedback.

1.1-4

Changed as.matrix to data.matrix in earth.default -- grep for FIXED
Extended earth.Rd slightly

1.1-2

Added my web page to DESCRIPTION and to some man pages

1.1-1

Changed \r\n to \n to pacify CMD CHECK

1.1-0

Default minspan is now 1 (was 0)
Fixed potential crash in PrintForwardStep if nTrace>1
Added a missing drop=FALSE to backward()
Minor code, comment, and man page fixups

1.0-8

Fixed bug where plotmo failed under these circumstances:
form <- Volume ~ .; a <- earth(form, data = trees); plotmo(a)

1.0-7

Minor change to summary.earth formatting.  Man page fixes.

1.0-6  May 11 2007

Initial release
